Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine

Authors: ZELLER, MICHAEL - Iowa State University; CHANG, JENNIFER - Orise Fellow; Baker, Amy; GAUGER, PHILLIP - Iowa State University; Anderson, Tavis

Submitted to: Virus Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2021
Publication Date: 10/8/2021
Citation: Zeller, M.A., Chang, J., Baker, A.L., Gauger, P.C., Anderson, T.K. 2021. Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine. Virus Evolution. 7(2). Article veab090. https://doi.org/10.1093/ve/veab090.
DOI: https://doi.org/10.1093/ve/veab090

Interpretive Summary: Influenza A virus (IAV) is an important respiratory pathogen in swine with significant economic losses due to decreased rate of gain, increased antibiotic and vaccine costs, and increased mortality. IAV in swine may be classified to one of three subtypes, H1N1, H1N2 and H3N2, but there is extensive diversity within each of these groups. Vaccine strategies to control infection have focused on the hemagglutinin (HA) protein, but efficacy is challenged by continual genetic change that interferes with vaccine-induced immunity or prior infection. An approach to increase the breadth and depth of vaccine protection is to include a neuraminidase (NA) protein that reflects the diversity of genes circulating in swine. Our study genetically characterized N2 NA genes circulating between 2010 and 2018 in US swine. These data revealed increases in the diversity of the N2 gene, with continual circulation of multiple genetic groups. We identified how NA genes may be preferentially paired with different HA genes and demonstrate how the NA-HA pairing results in rapid evolutionary changes in both proteins. These data also showed how the interstate movement of pigs and their viruses resulted in novel NA-HA pairings, and this movement spurred rapid changes in genetic diversity, along with the introduction of novel genes into new regions. Understanding NA genetic diversity in swine IAV has important implications for effective vaccine design: our study develops new classifications for N2 genes, demonstrates how NA-HA evolution are paired, and provides critical information for manufacturers and producers on how to objectively develop better vaccines with field-relevant components.

Technical Abstract: The neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (IAV) are essential surface glycoproteins. In this study, the evolution of subtype N2 NA paired with H1 and H3 subtype HA in swine was evaluated to understand if genetic diversity of HA and NA were linked in swine. Using time-scaled Bayesian phylodynamic analyses, the relationships of paired swine N2 with H1 or H3 from 2009 to 2018 were evaluated. These data demonstrated increased relative genetic diversity within the major N2 clades circulating in swine (N2.1998 between 2014-2017 and N2.2002 between 2010-2016). Relative genetic diversity of NA-HA pairs (e.g., N2.1998B/ H1.Delta1B) were correlated, suggesting inter-gene epistasis. Preferential pairing was observed among specific NA and HA genetic clades and this was associated with gene reassortment between cocirculating influenza A strains. Using the phylogenetic topology of inferred N2 trees, the expansion of genetic diversity in the NA gene was quantified and increases in diversity were observed subsequent to NA-HA reassortment events. The rate of evolution among NA-N2 clades and HA-H1 and HA-H3 clades were similar. The frequent regional movement of pigs and their influenza viruses is a possible explanation driving this pattern of drift, reassortment, and rapid evolution. Bayesian phylodynamic analyses demonstrated strong spatial patterns in N2 genetic diversity, and that frequent interstate movement of N2 clades homogenized diversity. The reassortment and evolution of NA and its influence on HA evolution may affect antigenic drift, impacting vaccine control programs and animal health.